source leaprc.protein.ff14SB
source leaprc.water.tip3p
loadamberparams frcmod.ionsjc_tip3p
loadamberparams  frcmod.ions1lm_126_tip3p
ache = loadPdb "ache-amber.pdb"
bond ache.66.SG ache.93.SG
bond ache.253.SG ache.264.SG
bond ache.401.SG ache.520.SG
check ache
#addions ache Na+ 0
#solvateOct ache TIP3PBOX 14.0
#addIons2 ache Cl- 4
#saveAmberParm ache solvated_ache.top solvated_ache.crd
quit 
